It is difficult to predict the measurement bias arising from the compliance of the atomic force microscope (AFM) probe. The issue becomes particularly important in this situation where nanometer uncertainties are sought for measurements with dimensional probes composed of flexible carbon nanotubes mounted on AFM cantilevers. We have developed a finite element model for simulating the mechanical behavior of AFM cantilevers with carbon nanotubes attached. Spring constants of both the nanotube and cantilever in two directions are calculated using the finite element method with known Young's moduli of both silicon and multiwall nanotube as input data. Compliance of the nanotube-attached AFM probe tip may be calculated from the set of spring constants. This paper presents static models that together provide a basis to estimate uncertainties in linewidth measurement using nanotubes. In particular, the interaction between a multiwall nanotube tip and a silicon sample is modeled using the Lennard-Jones theory. Snap-in and snap-out of the probe tip in a scanning mode are calculated by integrating the compliance of the probe and the sample-tip interacting force model. Cantilever and probe tip deflections and points of contact are derived for both horizontal scanning of a plateau and vertically scanning of a wall. The finite element method and the Lennard-Jones model provide a means to analyze the interaction of the probe and sample and measurement uncertainty, including actual deflection and the gap between the probe tip and the measured sample surface. SCANNING 30: 47–55, 2008. © 2008 Wiley Periodicals, Inc.